Earlier on Tuesday delegates to the United Russia congress unanimously approved Putin's candidacy for the position, which will offer strategic control over the party, holding an overwhelming majority in the lower house of parliament.
The Kremlin-backed party announced the new position of chairman, created for Putin, on Monday.
Speaking at the party's congress, Putin said, "I am grateful to accept the proposal made by party members and leaders."
"The party congress's decision ... will come into force after the president-elect is sworn in and I hand over presidential powers," he said.
Putin's protege, Dmitry Medvedev, will be inaugurated on May 7.
Speaking at the congress after accepting the offer, Putin called for the party to be reformed, to make it more open to debate. He said party should be purged of people pursuing their own narrow interests.
United Russia has long been criticized for being merely a Kremlin tool in parliament, with large numbers of bureaucrats and businessmen seeking lucrative connections.
On Tuesday, Putin again turned down an offer of membership in the party, as did Medvedev.
Putin, who has enjoyed unfading popularity throughout his two terms of office, helped United Russia win about 70% of the parliamentary vote in December by putting his name at the top of the party election list. But he has repeatedly refused to become a party member saying the head of state should not be affiliated with any party.
Analysts have suggested Putin could retain the strings of power under Medvedev, being in control of parliament, the economy and regions. Recent media reports said influential presidential envoys to provinces could be made accountable to the government.
With United Russia holding two thirds of State Duma seats, Putin could prevent the president from passing legislation through parliament.
Putin earlier said that as prime minister he would not have any powers not enjoyed by the current premier. Both Putin and Medvedev said they would work in tandem.